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- PDB-5ira: Expanding Nature's Catalytic Repertoire -Directed Evolution of an... -

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Basic information

Entry
Database: PDB / ID: 5ira
TitleExpanding Nature's Catalytic Repertoire -Directed Evolution of an Artificial Metalloenzyme for In Vivo Metathesis
ComponentsArtificial Metathesase
Keywordsbiotin-binding protein / beta barrel / metathesis / organometallic complex
Function / homologyAvidin-like / Lipocalin / Beta Barrel / Mainly Beta / Chem-9RU
Function and homology information
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHeinisch, T. / Jeschek, M. / Reuter, R. / Trindler, C. / Panke, S. / Ward, T.R.
CitationJournal: Nature / Year: 2016
Title: Directed evolution of artificial metalloenzymes for in vivo metathesis.
Authors: Jeschek, M. / Reuter, R. / Heinisch, T. / Trindler, C. / Klehr, J. / Panke, S. / Ward, T.R.
History
DepositionMar 12, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Oct 5, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Artificial Metathesase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2902
Polymers16,5701
Non-polymers7201
Water1,17165
1
A: Artificial Metathesase
hetero molecules

A: Artificial Metathesase
hetero molecules

A: Artificial Metathesase
hetero molecules

A: Artificial Metathesase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1598
Polymers66,2804
Non-polymers2,8794
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area9430 Å2
ΔGint-57 kcal/mol
Surface area19970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.496, 57.496, 183.415
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-316-

HOH

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Components

#1: Protein Artificial Metathesase


Mass: 16570.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-9RU / [1-[4-[[5-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]methyl]-2,6-dimethyl-phenyl]-3-(2,4,6-trimethylphenyl)-4,5-dihydroimidazol-1-ium-2-yl]-bis(chloranyl)ruthenium


Mass: 719.731 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H41Cl2N5O2RuS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 1.5 M AmSO4, 0.1 M Na acetate, pH4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999989 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999989 Å / Relative weight: 1
ReflectionResolution: 1.5→45.85 Å / Num. obs: 25264 / % possible obs: 100 % / Redundancy: 21.2 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 26.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 19.1 % / Rmerge(I) obs: 1.228 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QCB

2qcb


Resolution: 1.5→45.85 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.995 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.055 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.174 1269 5 %RANDOM
Rwork0.135 ---
obs0.137 23966 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20 Å2
2---0.57 Å20 Å2
3---1.15 Å2
Refinement stepCycle: LAST / Resolution: 1.5→45.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms913 0 42 65 1020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.021009
X-RAY DIFFRACTIONr_bond_other_d0.0020.02848
X-RAY DIFFRACTIONr_angle_refined_deg2.6751.9591390
X-RAY DIFFRACTIONr_angle_other_deg2.00231943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8295127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.04924.14641
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64215133
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.973154
X-RAY DIFFRACTIONr_chiral_restr0.1860.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021173
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02237
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9012.291493
X-RAY DIFFRACTIONr_mcbond_other3.8622.281492
X-RAY DIFFRACTIONr_mcangle_it4.553.431616
X-RAY DIFFRACTIONr_mcangle_other4.5483.44617
X-RAY DIFFRACTIONr_scbond_it5.6462.677515
X-RAY DIFFRACTIONr_scbond_other4.2312.603462
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0573.757693
X-RAY DIFFRACTIONr_long_range_B_refined6.26120.2511179
X-RAY DIFFRACTIONr_long_range_B_other5.19319.1421099
X-RAY DIFFRACTIONr_rigid_bond_restr5.68331854
X-RAY DIFFRACTIONr_sphericity_free25.014523
X-RAY DIFFRACTIONr_sphericity_bonded14.15351869
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 85 -
Rwork0.192 1741 -
obs--99.84 %

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